KOLKATA: Labs across the city that conducts Covid-19 tests are set to be more stringent in taking down the travel history of the person whose samples will undergo the test. This stricter vigil comes in the wake of the Omicron threat. The latest variant of SARS-CoV2 has already been detected in at least 15 countries. No case, however, has been detected in India so far.
“Taking down the travel history has become all the more important now that the Omicron threat looms. If we get a sample testing positive and the sample belongs to a person who has had a recent travel history to any of those countries where Omicron has surfaced, we can send those samples for genome sequencing,” said microbiologist Bhaskar Narayan Chaudhuri, who is attached with the lab at Peerless Hospital.
Since the mutation in Omicron has happened in the S-gene, a sample positive for this variant will have the S-gene missing. WHO had suggested that countries using PCR test containing the S-gene could utilise the S-gene target failure, an indicator for infection by Omicron subject to confirmation by genome sequencing.
But the ICMR-approved RT-PCR kits that most labs across the country, including those in Kolkata, are using currently do not include the S-gene. These kits mostly target two genes – N and ORF — and not the S-gene. But doctors said that these kits are capable of detecting all variants of SARS-Cov2, including Omicron.
“The RT-PCR kits that we are using currently will pick up the Covid-19 infection even if it has been caused by Omicron. The only thing is that since these RT-PCR kits do not target the S-gene, it will not throw any indication of which variant has caused the infection. Detecting the variant is all about sequencing, which is significant epidemiologically. But the treatment, isolation and other protocols remain same for all variants. We should be alert but not get panicked,” said microbiologist Shelly Sharma Ganguly attached with AMRI Hospitals.
“Omicron comes with more than 30 mutations in the spike. So its almost a different spike that it uses to engage ACE2. Does this increase transmission? We'll have to wait and see. Definitely, RT-PCR tests targeting the original spike sequence may show negative results, although usually these are paired with another gene of the virus. I feel in cases with discrepancies between the two targets should warrant sequencing in the index case, that means the discernible contact for each cluster of infection,” said immunologist Dipyaman Ganguly, a scientist at the Indian Institute of Chemical Biology.
Labs across the city admitted that if RT-PCR kits had targeted more genes, including the S-gene, it could have been useful in indirectly picking out possible infection by Omicron. But such kits are at least three times costlier than the ones currently being used. And since there is a capping on RT-PCR test rate, no private lab is likely to procure the more advanced kits.
